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- PDB-7ei2: Structure of human NNMT in complex with macrocyclic peptide 8 -

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Basic information

Entry
Database: PDB / ID: 7ei2
TitleStructure of human NNMT in complex with macrocyclic peptide 8
Components
  • Nicotinamide N-methyltransferase
  • macrocyclic peptide 8
KeywordsTRANSFERASE / Nicotinamide N-methyltransferase
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of protein deacetylation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / Methylation / : / positive regulation of gluconeogenesis / methylation / cytosol
Similarity search - Function
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / : / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsHayashi, K. / Mikamiyama, H. / Uehara, S. / Yamamoto, S. / Cary, D. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. ...Hayashi, K. / Mikamiyama, H. / Uehara, S. / Yamamoto, S. / Cary, D. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. / Kawai, T. / Ono, T. / Yamamoto, S. / Fumoto, M.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Macrocyclic Peptides as a Novel Class of NNMT Inhibitors: A SAR Study Aimed at Inhibitory Activity in the Cell.
Authors: Hayashi, K. / Uehara, S. / Yamamoto, S. / Cary, D.R. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. / Kawai, T. / Ono, T. / Yamamoto, S. / Fumoto, M. / Mikamiyama, H.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide N-methyltransferase
B: macrocyclic peptide 8


Theoretical massNumber of molelcules
Total (without water)30,0672
Polymers30,0672
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-7 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.693, 67.645, 44.300
Angle α, β, γ (deg.)90.000, 104.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 28891.164 Da / Num. of mol.: 1 / Mutation: E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli (E. coli)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Protein/peptide macrocyclic peptide 8


Mass: 1175.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium iodide, 0.1M Bis-Tris propane pH7.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.08→52 Å / Num. obs: 14497 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Χ2: 1.066 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.08-2.156.30.3814550.9410.1610.4130.97999.8
2.15-2.246.90.30314490.9710.1240.3281.034100
2.24-2.347.10.23614440.9780.0960.2551.055100
2.34-2.477.10.17614130.9870.0710.191.083100
2.47-2.627.20.13414680.9930.0540.1441.199100
2.62-2.827.20.10314280.9940.0410.1111.139100
2.82-3.117.30.07814510.9970.0310.0841.068100
3.11-3.567.30.05414500.9980.0220.0590.999100
3.56-4.487.30.03814690.9990.0150.0410.979100
4.48-507.10.02914700.9990.0120.0321.11699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.464
Highest resolutionLowest resolution
Rotation30.86 Å2.36 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREP11.6.02phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ROD

3rod


Resolution: 2.08→51.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.809 / SU ML: 0.155 / SU R Cruickshank DPI: 0.2242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 701 4.8 %RANDOM
Rwork0.184 ---
obs0.187 13794 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.06 Å2 / Biso mean: 46.734 Å2 / Biso min: 28.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0.02 Å2
2---0.07 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.08→51.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 0 68 1951
Biso mean---48.61 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191946
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9982641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.575241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14724.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30315321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.828157
X-RAY DIFFRACTIONr_chiral_restr0.110.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211458
LS refinement shellResolution: 2.08→2.133 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 48 -
Rwork0.242 998 -
all-1046 -
obs--98.87 %

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